Preheat oven to 350 degrees F (175 degrees C). Grease and flour muffin pans or use paper liners.
Whisk together the pumpkin puree, eggs, oil, applesauce, and sugar in a bowl. Combine the all-purpose flour, pastry flour, baking soda, and baking powder in a separate bowl. Slowly add the flour mixture to the pumpkin mixture, whisking continually. Fold in the coconut and chocolate chips. Pour the resulting batter into the muffin pans.
Bake in preheated oven until a toothpick inserted in the center of a muffin comes out clean, 15 to 20 minutes. Allow to cool completely on a wire rack before serving, about 1 hour.